Sandbox Eric Martz

This article is under collaborative development by Eric Martz (UMass) and Raymond J. Deshaies and his team (CalTech). Please do not edit this page unless you are a member of the development team. Once completed, this page may be moved to a permanent article title.

Proposed article title: Release of RING from Cullin by NEDD8ylation



 set backgroundmodel none; spin off; anim off; frame 0; Dimer 

 set backgroundmodel none; spin off; anim off; frame 7-8; Trimer 

 spin off; set backgroundmodel 1.9; anim mode palindrome; frame range 1.1 1.8;frame play; Animate Morph 

RING (A) Cullin (C) NEDD8 (A) 

Display chains A/C/R as smoothed backbone traces colored by N->C Rainbow:

 select *a; spacefill off; trace 0.5; color trace group; NEDD8 (A) </jmolButton>

 select *c; spacefill off; trace 0.5; color trace group; Cullin (C) </jmolButton>

 select *r; spacefill off; trace 0.5; color trace group; RING (R) </jmolButton>

 select protein; spacefill; Spacefill All </jmolButton>

Color traces by chain:

 select *a; spacefill off; trace 0.5; color trace [xa03000]; NEDD8 (A) </jmolButton>

 select *c; spacefill off; trace 0.5; color trace [xb08090]; Cullin (C) </jmolButton>

 select *r; spacefill off; trace 0.5; color trace [xa04090]; RING (R) </jmolButton>

<font color='#a04090'>RING (A) <font color='#b0a090'>Cullin (C) <font color='#a03000'>NEDD8 (A) </b>

The morph button above shows the transition from a Cullin-RING ligase dimer (3dpl) to the trimer resulting from NEDD8ylation (covalent addition of the NEDD8 ubiquitin-like chain to Lys724 of Cullin; 3dqv). NEDD8 binds and rotates the C-terminal domain of Cullin, releasing the folded RING domain from its Cullin-binding site. RING remains attached to Cullin by the RING N-terminus which remains embedded in Cullin. The contraction and re-expansion of the C-terminal domain during rotation is an artifact of the morphing algorithm.

Cullin atoms within 4.0 &Aring; of:

 select leu713:c.cd1, lys492:c.nz, arg495:c.ne, arg495:c.nh2; select selected or glu762:c, his763:c.cd2, his763:c.ce1, his763:c.ne2; spacefill; color cpk; RING (R) in dimer </jmolButton>

Colored by Element:

Use the buttons above to show Cullin as a trace in order to see these contacting atoms, then animate the morph. This shows that although the same long alpha helix contacts both RING and NEDD8, the Cullin atoms contacting RING do not, for the most part, contact NEDD8. Important Caveat: The dimer model lacks coordinates for residues 64-66 of RING (<font color='#00e000'>green in the N->C Rainbow), which are likely part of the Culllin-RING contact.

Flexibility of Trimer
<scene name='Sandbox_Eric_Martz/Trimer_morph/1'>Load and Animate Trimer Morph.

The model 3dqv contains two copies of the trimer in the asymmetric unit. Morphing one to the other shows flexibility of the trimer. The position of RING changes the most because of its flexible tether to Cullin. The two positions of RING in the crystal structure are undoubtedly stabilized by different crystal contacts (not shown here, but could be shown).

To reload the NEDD8ylation morph into Jmol above, simply reload this page.